关键词: 君子兰, 叶绿体基因组, 简单序列重复, 系统发育分析, ycf2

Abstract: The total DNA of Clivia miniata leaves was sequenced by Illumina MiSeq sequencing platform，and the full-length sequence（158 114 bp）of chloroplast genome（cpDNA）was obtained by assembly. A total of 135 genes were annotated in the cpDNA. The 135 genes included 87 protein coding genes，40 tRNA genes and 8 rRNA genes. Both simple sequence repeat（SSR）and codon preference of the cpDNA were analyzed using bioinformatics method. The results showed that（1）the total number of SSR loci in the cpDNA of C. miniata was 61，of which 38，9，2，8，3 and 1 were mononucleotide，dinucleotide，tirnucleotide，tetranucleotide，pentanucleotide and hexanucleotide repeats，respectively，and most of the SSRs were located in the intergenic regions；（2）the codons in cpDNA of C. miniata tended to end with A or U(T)，the frequency of serine was the highest and that of cysteine was the lowest. In addition，the phylogenetic analysis was carried out based on the full sequence of 24 cpDNAs and the sequence of 23 ycf2 genes of chloroplasts. The results showed that both C. miniata and Amaryllidaceae plants were clustered into one branch，which not only indicated the closest genetic relationship of them but also supported that C. miniata belongs to Amaryllidaceae. The results of phylogenetic analysis based on chloroplast ycf2 are mostly the same as that based on full sequence of cpDNA，which indicated that the ycf2 genes could replace full-length cpDNAs for plant phylogenetic analysis.

Key words: Clivia miniata, chloroplast genome, simple sequence repeat（SSR）, phylogenetic analysis, ycf2